Coarse-Grained Modeling and Simulations of Thermoresponsive …
67
current form. In such cases, the model will need to be modified to introduce either
both acceptor and donor beads on one monomer bead allowing for both inter and
intra-associations or model the polymer chain as being composed of two types of
monomer beads, those containing acceptor beads and those containing donor beads,
respectively, allowing it to selectively form intra-chain h-bonds. Second, specificity
is largely dependent on the chosen potential parameters namely the placement of
the A-A and D-D repulsive shell relative to the range of A-D attractive interaction
potential and care must be taken to optimize the value of σ AA /σ DD if formation of
A-D-A or D-A-D trimers is noted unless one wishes to model chemistries where such
trimers are expected to form. Lastly, as mentioned in the model section, one may
wish to include dihedral (A-G-G-A or D-M-M-D) interactions to be more realistic
and incorporate the torsional restraint placed on the backbone as the monomer makes
h-bonds with another monomer.
5 Conclusions
In conclusion, with the above biological (nucleic acids, peptides) and synthetic
polymer systems as examples, we have shown the reader the advantages, capabilities and limitations of such minimalist h-bonding polymer coarse-grained models.
By providing the essential model details for these three diverse macromolecular
systems and potential future directions, we have also demonstrated to the reader how
to modify or tailor these models to represent other macromolecular systems.
Acknowledgements The authors thank National Science Foundation (NSF)-DMR 1420736 for
financial support that led to the nucleic acid simulation results, NSF-CBET 1703402 for financial
support that led to the collagen-like peptide simulation results, and U.S. Department of Energy
Office of Science grant number DE-SC0017753 for financial support that led to the polymer
nanocomposites results presented in this contribution. The coarse grained models described in
Sect. 2 and 3 have been disseminated for other users via mosdef.org, a platform whose development
is supported by National Science Foundation (NSF) Grant 1835613. The authors also acknowledge
the use of information technologies resources at the University of Delaware, specifically the Farber
high-performance computing resources.
References
1. Chen S, Binder WH (2016) Dynamic ordering and phase segregation in hydrogen-bonded
polymers. Acc Chem Res 49(7):1409–1420
2. Heo K, Miesch C, Emrick T, Hayward RC (2013) Thermally reversible aggregation of gold
nanoparticles in polymer nanocomposites through hydrogen bonding. Nano Lett 13(11):5297–
5302
3. Montarnal D, Delbosc N, Chamignon C, Virolleaud M-A, Luo Y, Hawker CJ, Drockenmuller E, Bernard J (2015) Highly ordered nanoporous films from supramolecular diblock
copolymers with hydrogen-bonding junctions. Angew Chem Int Ed 54(38):11117–11121
67
current form. In such cases, the model will need to be modified to introduce either
both acceptor and donor beads on one monomer bead allowing for both inter and
intra-associations or model the polymer chain as being composed of two types of
monomer beads, those containing acceptor beads and those containing donor beads,
respectively, allowing it to selectively form intra-chain h-bonds. Second, specificity
is largely dependent on the chosen potential parameters namely the placement of
the A-A and D-D repulsive shell relative to the range of A-D attractive interaction
potential and care must be taken to optimize the value of σ AA /σ DD if formation of
A-D-A or D-A-D trimers is noted unless one wishes to model chemistries where such
trimers are expected to form. Lastly, as mentioned in the model section, one may
wish to include dihedral (A-G-G-A or D-M-M-D) interactions to be more realistic
and incorporate the torsional restraint placed on the backbone as the monomer makes
h-bonds with another monomer.
5 Conclusions
In conclusion, with the above biological (nucleic acids, peptides) and synthetic
polymer systems as examples, we have shown the reader the advantages, capabilities and limitations of such minimalist h-bonding polymer coarse-grained models.
By providing the essential model details for these three diverse macromolecular
systems and potential future directions, we have also demonstrated to the reader how
to modify or tailor these models to represent other macromolecular systems.
Acknowledgements The authors thank National Science Foundation (NSF)-DMR 1420736 for
financial support that led to the nucleic acid simulation results, NSF-CBET 1703402 for financial
support that led to the collagen-like peptide simulation results, and U.S. Department of Energy
Office of Science grant number DE-SC0017753 for financial support that led to the polymer
nanocomposites results presented in this contribution. The coarse grained models described in
Sect. 2 and 3 have been disseminated for other users via mosdef.org, a platform whose development
is supported by National Science Foundation (NSF) Grant 1835613. The authors also acknowledge
the use of information technologies resources at the University of Delaware, specifically the Farber
high-performance computing resources.
References
1. Chen S, Binder WH (2016) Dynamic ordering and phase segregation in hydrogen-bonded
polymers. Acc Chem Res 49(7):1409–1420
2. Heo K, Miesch C, Emrick T, Hayward RC (2013) Thermally reversible aggregation of gold
nanoparticles in polymer nanocomposites through hydrogen bonding. Nano Lett 13(11):5297–
5302
3. Montarnal D, Delbosc N, Chamignon C, Virolleaud M-A, Luo Y, Hawker CJ, Drockenmuller E, Bernard J (2015) Highly ordered nanoporous films from supramolecular diblock
copolymers with hydrogen-bonding junctions. Angew Chem Int Ed 54(38):11117–11121